We investigated the interactions between snowpack chemistry, mercury Hg contamination and microbial community structure and function in Arctic snow. Snowpack chemistry inorganic and organic ions including mercury Hg speciation was studied in samples collected during a two-month field study in a high Arctic site, Svalbard, Norway 79°N. Shifts in microbial community structure were determined by using a 16S rRNA gene phylogenetic microarray. We linked snowpack and meltwater chemistry to changes in microbial community structure by using co-inertia analyses CIA and explored changes in community function due to Hg contamination by q-PCR quantification of Hg-resistance genes in metagenomic samples. Based on the CIA, chemical and microbial data were linked p = 0.006 with bioavailable Hg BioHg and methylmercury MeHg contributing significantly to the ordination of samples. Mercury was shown to influence community function with increases in merA gene copy numbers at low BioHg levels. Our results show that snowpacks can be considered as dynamic habitats with microbial and chemical components responding rapidly to environmental changes.